Motorcycle Repair: Electrical problem with 03 HD 883 Custom, softtail custom, screaming eagle exhaust

Question
Bought this 03 HD 883 Custom last week -  ride home from previous owner uneventful.  Bike has 2050 miles on it - had drag pipes  - knew they would not pass inspection in Maryland = removed and installed Screaming Eagle exhaust.  Tried to ride bike this weekend - started fine...idles fine...after warmup of about 10 minutes... rough running and speedometer and lights flicker on and off - looses one cylinder ?  bike runs very rough...then it clears out and idles fine.  Removed battery and cleaned terminals.  I do not have a service manual for this model. (Husband owns a 04 Softtail Custom...would that manual help in any way ?  Thanks!

Answer
Your going to have to get a manual for your bike. the softtail wont help much. Sounds like you have a short somewhere. With the speedo light flickering I would start with the lighting system and look there, although the flickering mught be caused by the rough idleing. Does the headlight flicker as well?
Mike